During stem cell differentiation, genes related to their unique characters should be silenced and genes related to the target lineage must be activated. Epigenetics is well known to control gene expression and changes of the epigenetic status during differentiation were reported. Epigenetic modifiers are chemical agents that can remove the epigenetic silencing markings and consequently activate the affected genes. The role of the epigenetic modifiers is well established in cancer treatment. Reports about enhancing stem cells differentiation (both murine and human) with treatment of the modifiers are accumulating. The modifiers have no differentiation ability by themselves but they enhance the differentiation upon culturing the cells in the corresponding conditions. This effect has been shown in monolayer culture as well as three-dimensional pellets. Epigenetic modifiers could be a valuable additive to the classical differentiation protocols, although various questions have yet to be answered including the safety of the agents.